Re: AMBER: pmemd install error

From: Robert Duke <>
Date: Tue, 23 Jan 2007 08:01:46 -0500

Ji-Lai -
OpenMPI is not MPICH. You installed pmemd as if there was an MPICH environment available. So if you must use OpenMPI, you must figure out the correct library names and their locations as well as the location of the OpenMPI include files, and modify the appropriate information in your pmemd config.h file. You must also make sure that OpenMPI has been built with ifort specified as the fortran compiler. Since sander does support OpenMPI, a fairly simple way to do all this is to build parallel sander, then look at the config.h that was used under $AMBERHOME/src.
This basic question has come up before, so there may be folks out there with more specific information. I made the decision to not support OpenMPI in the amber 9 release because it was not yet widely used and the documentation available was really thin - both of which are recipes for trouble (folks on the bleeding edge of things tend to bleed a lot...).
Best Regards - Bob Duke

----- Original Message -----
  From: Ji-Lai Li
  Sent: Tuesday, January 23, 2007 1:59 AM
  Subject: AMBER: pmemd install error

  Dear Users:
     I can't install PMEMD in my machine: Linux x86_64. The MPI is openmpi, and the environment variable was set to:
  ##Open MPI
  setenv MPI_HOME /home/mds/progpack/openmpi-1.1.3/build/
  setenv MPI_INCLUDE /home/mds/progpack/openmpi-1.1.3/build/include
  setenv PATH /home/mds/progpack/openmpi-1.1.3/build/bin:$PATH
  setenv LD_LIBRARY_PATH /home/mds/progpack/openmpi- 1.1.3/build/lib:$LD_LIBRARY_PATH
  setenv MPILIB "-L$LD_LIBRARY_PATH -lmpich"

  when I type in /home/mds/amber9/src/pmemd/
  ./configure linux_em64t ifort mpich
  make install

  it prompts:
  ifort -c -auto -tpp7 -xW -ip -O3 parallel_dat.f90
  fortcom: Error: parallel_dat.f90, line 96: Cannot open include file 'mpif-common.h'
        include 'mpif-common.h'
  fortcom: Error: parallel_dat.f90, line 227: This name does not have a type, and must have an explicit type. [MPI_COMM_WORLD]
      call mpi_abort(mpi_comm_world, i, err_ret_code)
  compilation aborted for parallel_dat.f90 (code 1)
  make[1]: *** [parallel_dat.o] Error 1
  make[1]: Leaving directory `/home/mds/amber9/src/pmemd/src'
  make: *** [install] Error 2

  I confirmed the include file 'mpif-common.h' in /home/mds/progpack/openmpi-1.1.3/build/include.

  Does anyone know what I"m doing wrong?

  Ji-Lai Li

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jan 24 2007 - 06:07:37 PST
Custom Search